Software Presentations

2008     2007     2006     2005     2004     2003     2002     2001     2000     Pre-2000

Below are lectures, talks, and other presentations given by TCB staff, faculty, group members, and others in meetings and conferences locally and around the world about the TCB software applications VMD, NAMD, and BioCoRE.

2008

  • March 12, 2008, Atlanta, GA, SIAM Conference on Parallel Processing for Scientific Computing
    Lecture: "Accelerating Molecular Modeling Applications with Graphics Processors" (John Stone)

2007

  • November 9, 2007, Princeton, NJ, Princeton University, Institute for Advanced Study, AstroGPU 2007 Conference
    Lecture: "GPU Acceleration of Scientific Applications Using CUDA" (John Stone)

  • November 11, 2007, Reno, NV, SC07 International Conference on High Performance Computing, Networking, Storage, and Analysis
    Tutorial: "High Performance Computing on GPUs with CUDA" (John Stone)

  • October 15, 2007, Urbana, IL, University of Illinois, ECE 498L1: Programming Massively Parallel Processors
    Lecture: "Case Studies: Ion Placement Tool, VMD" (John Stone)

  • March 14, 2007, Urbana, IL, University of Illinois, ECE 498L1: Programming Massively Parallel Processors
    Lecture: "Case Studies: Ion Placement Tool, VMD" (John Stone)

2006

  • March 16-17, 2006, UIUC, Urbana, IL, Beckman Institute, TCBG Cluster Building Workshop
    Lecture: "Linux Clusters for High-Performance Computing: An Introduction" (Tim Skirvin)
    Lecture: "Linux Clusters: Details and Case Studies" (Jim Phillips, Tim Skirvin)

  • April 4, 2006, University of Texas Health Science Center at Houston
    Lecture: "Visualization of Nano-Scale Structures"

  • April 20-21, 2006, UIUC, Urbana, IL, Beckman Institute, TCBG Cluster Building Workshop
    Lecture: "Linux Clusters for High-Performance Computing: An Introduction" (Tim Skirvin, Jim Phillips)
    Lecture: "Linux Clusters: Details and Case Studies" (Jim Phillips, Tim Skirvin)

  • August 11, 2006, Universidad Nacional Autónoma de Mexico, DGSCA
    Lecture: "Visualization of Nano-Scale Structures"

  • November 30-December 1, 2006, UIUC, Urbana, IL, Beckman Institute, TCBG Cluster Building Workshop
    Lecture: "Linux Clusters for High-Performance Computing: An Introduction" (Tim Skirvin, Jim Phillips)
    Lecture: "Linux Clusters: Details and Case Studies" (Jim Phillips, Tim Skirvin)

2005

  • February 15, 2005, UIUC, Urbana, IL, Beckman Institute - Imaging Technology Group Forum
    Lecture: "Dancing Proteins: 3-D Visualization of Protein Structure and Dynamics on Next-Generation Graphics Hardware" (John Stone)
     

  • February 22, 2005, University of Missouri at Rolla, Rolla, MO, Department of Computer Science CS Colloquium
    Lecture: "Dancing Proteins: 3-D Visualization of Protein Structure and Dynamics on Next-Generation Graphics Hardware" (John Stone)
     

  • February 25, 2005, Purdue University, West Lafayette, IN, Envision Center
    Lecture: "Dancing Proteins: 3-D Visualization of Protein Structure and Dynamics on Next-Generation Graphics Hardware" (John Stone)
     

  • September 12, 2005, San Francisco, CA, UCSD, San Diego Supercomputer Center, Visualization of Large Biomolecular Complexes Workshop
    Lecture: "VMD: Algorithms and Methods for Large Scale Biomolecular Visualization" (John Stone)
     

  • September 22-23, 2005, UIUC, Urbana, IL, Beckman Institute, TCBG Cluster Workshop
    Lecture: "Linux Clusters for High-Performance Computing: An Introduction" (Tim Skirvin)
    Lecture: "Linux Clusters: Details and Case Studies" (Jim Phillips, Tim Skirvin)
     

  • October 25, 2005, Urbana, IL, UIUC CITES Computer Consultant Support Program Conference
    Lecture: "Linux Clustering for Scientific Computing" (ppt) (Jim Phillips, Tim Skirvin)
     

  • November 3, 2005, UIUC, Urbana, IL, National Center for Supercomputing Applications, Social Networks and Cyberinfrastructure Conference
    Lecture: "BioCoRE Overview" (Kirby Vandivort)
     

  • November 10-11, 2005, UIUC, Urbana, IL, Beckman Institute, TCBG Cluster Workshop
    Lecture: "Linux Clusters for High-Performance Computing: An Introduction" (Tim Skirvin)
    Lecture: "Linux Clusters: Details and Case Studies" (Jim Phillips, Tim Skirvin)
     

  • November 12-18, 2005, Seattle, WA, SC|05 International Conference for High Performance Computing, Networking, Storage and Analysis
    Presentation: "Exploring Biomolecular Machines with Supercomputers" (Jim Phillips, Jordi Cohen)

2004

  • March 23, 2004, Bologna, Italy, ScicomP 9 Conference
    Lecture: "Molecular Dynamics Applications: NAMD" (Angelo Rossi (IBM) and Joachim Hein (University of Edinburgh))
     
  • October 3-5, 2004, Arlington, VA, NSF Cyberenabled Chemistry Workshop
    Presentation: "BioCoRE" (Kirby Vandivort)
     
  • November 8-11, 2004, Pittsburgh, PA, IEEE/ACM SC2004 Conference
    Presentation: "Exploring Biomolecular Machines with Supercomputers" (James Phillips)
     
  • December 8-9, 2004, Nance, France, INRIA/CNRS ARC Docking Project
    Presentation: "VMD Biomolecular Visualization and Analysis" (John Stone)

2003

  • June 2, 2003, Melbourne, Australia, Terascale Performance Analysis Workshop, International Conference on Computational Science 2003
    Lecture: "Scaling Molecular Dynamics to 3000 Processors with Projections: A Performance Analysis Case Study"
          (Laxmikant V. Kale, Sameer Kumar, Gengbin Zheng, Chee Wai Lee)
     
  • July 12, 2003, La Jolla, CA, Joint Amber CHARMM Developer's Symposium
    Lecture: "University of Illinois Software Integration Opportunities" (James Phillips)
  • November 17-20, 2003, Phoenix, AZ, IEEE/ACM SC2003 Conference
    Presentation: "NAMD, VMD, and BioCoRE, NIH NCRR Booth" (James Phillips and Robert Brunner)
    Presentation: "BioCoRE: A Collaborative Work Environment for Biomedical Research, Research Management and Training" (Robert Brunner)
    Presentation: "VMD: Visual Molecular Dynamics" (Sun personnel)
    Presentation: "NAMD and VMD: Live Molecular Dynamics Simulation on a InfiniBand Opteron Cluster" (InfiniCon Systems personnel)

2002

  • February 2002, Biophysical Society Meeting
    Poster: "BioCoRE: A Biological Collaborative Research Environment" (Kirby Vandivort, Robert Brunner, Gila Budescu, Barry Isralewitz, Laxmikant V. Kale, Klaus J. Schulten)
     
  • March 8-9, 2002, Champaign-Urbana, IL, University of Illinois at Champaign-Urbana, Beckman Institute for Advanced Science and Technology Open House
    Lecture: "An Interactive Tour of the Living Cell"
     
  • April 17-19, 2002, NCSA, NAMD Workshop
    Lecture: "Introduction to Molecular Dynamics Simulations" (Klaus Schulten)
    Lecture: "What Can We Learn from MD Simulations?" (Klaus Schulten)
    Lecture: "Case Study: Unfolding the Muscle Protein Titin" (Mu Gao)
    Lecture: "Case Study: Aquaporin Membrane Channels" (Emad Tajkhorshid)
    Lecture: "Case Study: ATP Synthase Stalk Rotation" (Barry Isralewitz)
    Lecture: "Overview of Applicable Hardware and Software" (Jim Phillips)
    Lecture: "Configuring and Running NAMD Simulations" (Jim Phillips)
    Lecture: "Building Molecular Structures for NAMD" (Justin Gullingsrud)
    Lecture: "Assembling Molecular Systems for NAMD" (Justin Gullingsrud)
    Lecture: "Integrating the Equations of Motion" (Jim Phillips)
    Lecture: "Accelerating Processes via Steered MD" (Klaus Schulten)
    Lecture: "Analysis of MD Trajectories" (Justin Gullingsrud)
    Lecture: "Efficient Evaluation of Forces" (Jim Phillips)
    Lecture: "NAMD Serial and Parallel Performance" (Jim Phillips)
     
  • May 2002, Alliance All Hands Meeting
    Poster: "BioCoRE: A Biological Collaborative Research Environment" (Robert Brunner, Kirby Vandivort)
     
  • May 20, 2002, Pittsburgh, PA,  Scaling to New Heights Workshop at the Pittsburgh Supercomputing Center
    Lecture:  "NAMD: Biomolecular Simulations on Thousands of Processors"
     
  • July 23-25, 2002, Siggraph 2002 Exhibition
    Lecture: "Biomolecular Visualization"
     
  • August 5, 2002, Edmonton, Canada, 10th International Conference on Intelligent Systems for Molecular Biology
     Lecture: "BioCoRE: A Biological Collaborative Research Environment" (Kirby Vandivort)
     

  • September 16-18, 2002, Ballston, VA, Data and Collaboratories in the Biomedical Community Workshop
    Lecture:  "BioCoRE: A Collaboratory for Structural Biology" (Gila Budescu)
     

  • October 22, 2002, Champaign, IL, NCSA Access Grid Seminar Series
     Lecture: "BioCoRE: A Biological Collaborative Research Environment" (Robert Brunner, Kirby Vandivort)
     
  • November 18-22, 2002, Baltimore, MD, IEEE/ACM SC2002 Exhibition
    Lecture: "NAMD and VMD: Live Molecular Dynamics Simulation and Visualization on NCSA Itanium Linux Cluster and Tiled Display Wall" (Jim Phillips)
    Lecture: "NAMD and VMD: Interactive Molecular Dynamics Simulation" (Sun personnel)
    Paper: "NAMD: Biomolecular Simulation on Thousands of Processors - Gordon Bell Award Finalist NAMD Paper"

2001

  • June 19, 2001
    Lecture: "NAMD Linux Cluster Tutorial" (Jim Phillips, Tim Skirvin, John Stone)
     
  • June 26, 2001, NCSA Linux Revolution Conference
    Lecture: "NAMD Linux Cluster Tutorial" (Jim Phillips, Tim Skirvin, John Stone)
     
  • July 13, 2001
    Lecture: "NAMD Linux Cluster Tutorial" (Jim Phillips, Tim Skirvin, John Stone)
     
  • August 14-16, 2001, Siggraph 2001 Exhibition
    Lecture: "VMD - Visual Molecular Dynamics"
     
  • August 15-18, 2001, Pittsburgh, PA, Mellon Institute Building, Pittsburgh Supercomputing Center (PSC), PSC NAMD Workshop 2001
    Lecture: "Hands-On: Viewing Molecules with VMD" (Justing Gullingsrud)
    Lecture: "Introduction to MD Simulations" (Klaus Schulten)
    Lecture: "Semi empirical Force Fields and Their Limitations" (Ioan Kosztin)
    Lecture: "Configuring and Running NAMD Simulations" (Jim Phillips)
    Lecture: "Hands-On: Simulation of BPTI at Different Temperatures" (Klaus Schulten)
    Lecture: "What Can We Learn from MD Simulations?" (Klaus Schulten)
    Lecture: "Case Study: Protein-Membrane Simulation" (Klaus Schulten)
    Lecture: "Analysis of MD results using Statistical Mechanics Methods" (Ioan Kosztin)
    Lecture: "Hands-On: Analysis of BPTI Equilibrium Properties" (Ioan Kosztin)
    Lecture: "Integrating the Equations of Motion" (Jim Phillips)
    Lecture: "Building Molecular Structures for NAMD" (Jim Phillips)
    Lecture: "Assembling Molecular Systems for NAMD" (Justin Gullingsrud)
    Lecture: "Hands-On: Assembly of Gramicidin in a Membrane" (Justin Gullingsrud)
    Lecture: "Efficient Evaluation of Forces" (Jim Phillips)
    Lecture: "Analysis of MD Trajectories" (Ioan Kosztin)
    Lecture: "Case Study: Signaling Proteins" (Ioan Kosztin)
    Lecture: "Hands-On: Equilibration of Gramicidin in a Membrane" (Justin Gullingsrud)
    Lecture: "NAMD Serial and Parallel Performance" (Jim Phillips)
    Lecture: "Case Study: Steered MD Simulation" (Justin Gullingsrud)
     
  • November 12-15, 2001, SC2001 Exhibition
    Lecture: "NAMD and VMD: Interactive Molecular Dynamics Simulation" (Jim Phillips)
    Lecture: "NAMD: Scalable Molecular Dynamics" (Jim Phillips)
    Lecture: "NAMD and VMD: Live Molecular Dynamics Simulation and Visualization on NCSA Itanium Linux Cluster and Tiled Display Wall" (Michelle Gower, NCSA)
    Lecture: "Theoretical Biophysics (TBG), NCSA and Intel McKinley Demo"
    Lecture: "BioCoRE Submits, Runs, and Visualizes your Simulations From Afar" (Kirby Vandivort)

2000

  • April 2000, University of Notre Dame, VMD - High Performance Molecular Visualization
     
  • April 2000, University of Missouri-Rolla, VMD - High Performance Molecular Visualization
     
  • April 27, 2000, UIUC Beckman Institute, Urbana, IL, Beckman Institute for Advanced Science and Technology ITG Forum
    Lecture:  "BioCoRE: A Collaboratory for Structural Biology, Imaging Technology Group Forum"
     
  • October 27-29, 2000, Pittsburgh, PA, NCRR Biomedical Collaboratories Workshop Pittsburgh Supercomputer Center.
Pre-2000
  • November 11, 1999, Champaign-Urbana, IL, University of Illinois at Champaign-Urbana, Beckman Institute for Advanced Science and Technology ITG Forum
    Lecture: "Linux Clusters" (Jim Phillips, John Stone)
     
  • November 1998, University of Missouri-Rolla, VMD - A Molecular Visualization System

 

footer